FIRMAGene: FIRMAGene - Finding Isoforms using Robust Multichip Analysis...

In FIRMAGene: FIRMAGene - differential splicing for Affymetrix Gene 1.0 ST

Description

Using auxiliary information from the RMA robust fit, differential splicing can be used

Usage

FIRMAGene(object, nSamples = 2000, seed = 1976, cls = NULL, verbose = TRUE, idsToUse = NULL, minProbes = 4) 

Arguments

object	a ProbeLevelModel object (from package aroma.affymetrix). In future, support will be added for PLMset
nSamples	number of random samples to take for simulated null distribution.
seed	seed for random number generator.
cls	variable giving the class (aligned with the columns or sample names of the input object).
verbose	logical, whether to display progress.
idsToUse	indices of the units to calculate FIRMAGene scores for.
minProbes	minimum number of probes to operate on.

Details

Basically, the following steps take place:

* gather the residual from the object in question * standardize the residuals * calculate the MUF (maximum partial sum) score for the observed data * calculate the MUF (maximum partial sum) score for the simulated null data * compare the observed scores to the null distibution

Value

'FGset' object

Author(s)

Mark Robinson

References

Robinson MD and Speed TP (2009). ...

See Also

topSplices

Examples

## not run
# hgnetaffx <- read.csv("HuGene-1_0-st-v1.na25.hg18.transcript.csv",sep=",",skip=19,header=TRUE,comment.char="")
# u <- which(getUnitNames(cdf) %in% hgnetaffx$probeset_id[hgnetaffx$category == "main" & hgnetaffx$total_probes > 7 & hgnetaffx$total_probes < 200])
# fg <- FIRMAGene(plm, idsToUse=u, cls=cls)

FIRMAGene documentation built on May 2, 2019, 5:55 p.m.